1. Introduction

OpenEye Scientific Software's substructure query tools are a suite of utilities for manipulating and converting patterns for searching molecular databases. These tools can convert substructure or reaction queries expressed in MDL file format (such as created using MDL's ISIS/Draw or CambridgeSoft's ChemDraw) to Daylight SMARTS strings (for example, for searching using Daylight Chemical Information Systems' DayCart or Merlin database systems).